|
REFMAC (CCP4: Supported Program)
User's manual for the program refmac_5.0.36
DICTIONARY
- Full Description of the dictionary files
-
- Description of organisation of the ligand dictionary used by the program REFMAC
- Dictionary entry from coordinate file(s)
- How to make a dictionary entry if there is a coordinate file. Coordinate file
formats recognised are PDB, small molecule CIF (for example when coordinates
are from the Cambridge small molecule database - CSD) or mmCIF
- Dictionary entry from minimum description
- How to make a dictionary entry by describing only a connectivity list and element names
- Interactive sketcher to make dictionary entry
- Using interactive sketcher which is part of CCP4 graphical user interface to make dictionary entry
- How to avoid the three letter residue name problem
- PDB residue names are restricted to three letters. This document describes how to avoid this
problem and not to break the PDB rule
- Retrieve coordinates from dictionary
- If the ligand is in the dictionary file supplied by us: how to retrieve coordinates
to start to build using graphics
- List of standard monomer descriptions
- List of ligand descriptions distributed with the program REFMAC
- Links to non-commercial editors to derive coordinates from
chemical description
- Links to various non-commercial web sites which can help to derive
coordinates from chemical descriptions. And these coordinates can be used to
derive a dictionary entry as well as for model (re)building
|